Good question. < and >
On Fri, Aug 3, 2012 at 10:56 AM, Dina Schneidman duhovka@gmail.com wrote:
> is there escape character for '<'? > > On Fri, Aug 3, 2012 at 10:45 AM, Daniel Russel drussel@gmail.com wrote: > > Generating the documentation produces a very large number of warnings. > These > > make it hard to find new problems introduced by changes, as well as, > > sometimes, representing real problems in the documentation (there are a > few > > warnings that I have not for the life of me been able to figure out what > is > > going on). It would be really nice if people could clean up the warnings > in > > the code they produce. To produce the documentation (and see the > warnings), > > you can do "scons doc". Note, the first time will take much longer than > > subsequent runs (graphs and equations gets cached between runs). And for > > convenience, I'm including the current set of warnings below. The main > > offenders are integrative_docking, isd, em, and multifit. Thanks very > much. > > > > To clarify some of the warnings: > > - < must be escaped if it is not an html tag > > - not all files are in the example path (only examples and the example > > module). This could change, but I'm not sure there is a good reason to > > > > > > > > build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:7: warning: Unsupported > > xml/html tag <exp_profile_file> found > > build/doxygen/integrative_docking/overview.dox:10: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:11: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:12: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:21: warning: Unsupported > > xml/html tag <exp_profile_file> found > > build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported > > xml/html tag <image1> found > > build/doxygen/integrative_docking/overview.dox:24: warning: Unsupported > > xml/html tag <image2> found > > build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:27: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:28: warning: Unsupported > > xml/html tag <image1> found > > build/doxygen/integrative_docking/overview.dox:28: warning: Unsupported > > xml/html tag <image2> found > > build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:31: warning: Unsupported > > xml/html tag <em_map> found > > build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:34: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:35: warning: Unsupported > > xml/html tag <em_map> found > > build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported > > xml/html tag <residue_content_file1> found > > build/doxygen/integrative_docking/overview.dox:38: warning: Unsupported > > xml/html tag <residue_content_file2> found > > build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:43: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:44: warning: Unsupported > > xml/html tag <residue_content_file1> found > > build/doxygen/integrative_docking/overview.dox:45: warning: Unsupported > > xml/html tag <residue_content_file2> found > > build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:55: warning: Unsupported > > xml/html tag <cross_links_file> found > > build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported > > xml/html tag <pdb1> found > > build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported > > xml/html tag <pdb2> found > > build/doxygen/integrative_docking/overview.dox:58: warning: Unsupported > > xml/html tag <trans_file> found > > build/doxygen/integrative_docking/overview.dox:59: warning: Unsupported > > xml/html tag <cross_links_file> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <file1> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <weight1> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <file2> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <weight2> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <file3> found > > build/doxygen/integrative_docking/overview.dox:72: warning: Unsupported > > xml/html tag <weight3> found > > > /usr/local/google/home/drussel/src/imp/imp/modules/librmf/doc/categories.dox:94: > > warning: Found unknown command `\rmfattribute' > > /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:683: > > warning: explicit link request to 'if' could not be resolved > > /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:812: > > warning: explicit link request to 'include' could not be resolved > > /usr/local/google/home/drussel/src/imp/imp/doc/developer_guide.dox:850: > > warning: unable to resolve reference to `close_pairs' for \ref command > > /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:318: warning: > > explicit link request to 'RMF::HDF5FloatDataSet2D' could not be resolved > > /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:167: warning: > > unable to resolve reference to `nup84_cg' for \ref command > > /usr/local/google/home/drussel/src/imp/imp/doc/history.dox:167: warning: > > unable to resolve reference to `nup84_rb' for \ref command > > /usr/local/google/home/drussel/src/imp/imp/doc/introduction.dox:316: > > warning: unable to resolve reference to `nup84_cg.py' for \ref command > > build/doxygen/atom/overview.dox:5: warning: found paragraph command > outside > > of subsubsection context! > > <unknown>:206: warning: unable to resolve reference to `B' for \ref > command > > build/include/IMP/em/rigid_fitting.h:300: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::compute_fitting_score(const ParticlesTemp &ps, DensityMap > *em_map, > > FloatKey wei_key=atom::Mass::get_mass_key(), bool local=false) > > build/include/IMP/em/rigid_fitting.h:300: warning: The following > parameters > > of IMP::em::compute_fitting_score(const ParticlesTemp &ps, DensityMap > > *em_map, FloatKey wei_key=atom::Mass::get_mass_key(), bool local=false) > are > > not documented: > > parameter 'local' > > build/include/IMP/em/rigid_fitting.h:250: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::compute_fitting_scores(const ParticlesTemp &ps, DensityMap > *em_map, > > const algebra::Transformation3Ds &transformations, bool > fast_version=false, > > bool local_score=false, const FloatKey > &wei_key=atom::Mass::get_mass_key()) > > build/include/IMP/em/rigid_fitting.h:277: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::compute_fitting_scores(DensityMap *em_map, core::RigidBody rb, > > Refiner *refiner, const algebra::Transformation3Ds &transformations, > const > > FloatKey &=atom::Mass::get_mass_key()) > > build/include/IMP/em/rigid_fitting.h:277: warning: argument 'wei_key' of > > command @param is not found in the argument list of > > IMP::em::compute_fitting_scores(DensityMap *em_map, core::RigidBody rb, > > Refiner *refiner, const algebra::Transformation3Ds &transformations, > const > > FloatKey &=atom::Mass::get_mass_key()) > > build/include/IMP/em/density_map_volumetrics.h:29: warning: argument > 'only' > > of command @param is not found in the argument list of > > IMP::em::get_molecular_mass_at_threshold(DensityMap *m, Float threshold, > > atom::ProteinDensityReference ref=atom::HARPAZ) > > build/include/IMP/em/density_map_volumetrics.h:29: warning: argument > 'the' > > of command @param is not found in the argument list of > > IMP::em::get_molecular_mass_at_threshold(DensityMap *m, Float threshold, > > atom::ProteinDensityReference ref=atom::HARPAZ) > > build/include/IMP/em/density_map_volumetrics.h:57: warning: argument > 'the' > > of command @param is not found in the argument list of > > IMP::em::get_threshold_for_approximate_mass(DensityMap *m, Float > > desired_mass, atom::ProteinDensityReference ref=atom::HARPAZ) > > build/include/IMP/em/DensityMap.h:582: warning: argument 'from' of > command > > @param is not found in the argument list of > > IMP::em::get_transformed_into(const DensityMap *source, const > > algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) > > build/include/IMP/em/DensityMap.h:582: warning: The following parameters > of > > IMP::em::get_transformed_into(const DensityMap *source, const > > algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) are > not > > documented: > > parameter 'source' > > build/include/IMP/em/density_map_volumetrics.h:19: warning: argument > > 'consider' of command @param is not found in the argument list of > > IMP::em::get_volume_at_threshold(DensityMap *m, Float threshold) > > build/include/IMP/em/rigid_fitting.h:102: warning: argument 'rb' of > command > > @param is not found in the argument list of > > IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner *refiner, > > const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D > > &anchor_centroid, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, > > bool fast=false) > > build/include/IMP/em/rigid_fitting.h:102: warning: argument 'radius_key' > of > > command @param is not found in the argument list of > > IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner *refiner, > > const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D > > &anchor_centroid, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, > > bool fast=false) > > build/include/IMP/em/rigid_fitting.h:102: warning: The following > parameters > > of IMP::em::local_rigid_fitting_around_point(Particle *p, Refiner > *refiner, > > const FloatKey &weight_key, DensityMap *dmap, const algebra::Vector3D > > &anchor_centroid, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3, > > bool fast=false) are not documented: > > parameter 'p' > > parameter 'refiner' > > build/include/IMP/em/rigid_fitting.h:189: warning: argument 'rb' of > command > > @param is not found in the argument list of > > IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner *refiner, > > const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds > > &anchor_centroids, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) > > build/include/IMP/em/rigid_fitting.h:189: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner *refiner, > > const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds > > &anchor_centroids, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) > > build/include/IMP/em/rigid_fitting.h:189: warning: The following > parameters > > of IMP::em::local_rigid_fitting_around_points(Particle *p, Refiner > *refiner, > > const FloatKey &wei_key, DensityMap *dmap, const algebra::Vector3Ds > > &anchor_centroids, OptimizerStates display_log, Int > > number_of_optimization_runs=5, Int number_of_mc_steps=10, Int > > number_of_cg_steps=100, Float max_translation=2., Float max_rotation=.3) > are > > not documented: > > parameter 'p' > > parameter 'refiner' > > build/include/IMP/em/rigid_fitting.h:219: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::local_rigid_fitting_grid_search(const ParticlesTemp &ps, const > > FloatKey &wei_key, DensityMap *dmap, Int max_voxels_translation=2, Int > > translation_step=1, Float max_angle_in_radians=0.174, Int > > number_of_rotations=100) > > build/include/IMP/em/converters.h:73: warning: argument 'rad_key' of > command > > @param is not found in the argument list of > > IMP::em::particles2binarized_density(const ParticlesTemp &ps, Float > > resolution, Float apix, int sig_cutoff=3, const FloatKey > > &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/em/converters.h:54: warning: argument 'rad_key' of > command > > @param is not found in the argument list of > IMP::em::particles2density(const > > ParticlesTemp &ps, Float resolution, Float apix, int sig_cutoff=3, const > > FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/em/converters.h:101: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::particles2surface(const ParticlesTemp &ps, Float apix, const > > FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvx' of > > command @param is not found in the argument list of > > IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, > SampledDensityMap > > *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, > > unsigned long eval_interval) > > build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvy' of > > command @param is not found in the argument list of > > IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, > SampledDensityMap > > *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, > > unsigned long eval_interval) > > build/include/IMP/em/CoarseCCatIntervals.h:32: warning: argument 'dvz' of > > command @param is not found in the argument list of > > IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, > SampledDensityMap > > *model_map, const algebra::Vector3Ds &deriv, float scalefac, bool lderiv, > > unsigned long eval_interval) > > build/include/IMP/em/CoarseCCatIntervals.h:32: warning: The following > > parameters of IMP::em::CoarseCCatIntervals::evaluate(DensityMap *em_map, > > SampledDensityMap *model_map, const algebra::Vector3Ds &deriv, float > > scalefac, bool lderiv, unsigned long eval_interval) are not documented: > > parameter 'deriv' > > build/include/IMP/em/DensityFillingRestraint.h:33: warning: The following > > parameters of > > IMP::em::DensityFillingRestraint::DensityFillingRestraint(Particles ps, > > DensityMap *em_map, Float threshold) are not documented: > > parameter 'threshold' > > build/include/IMP/em/DensityMap.h:582: warning: argument 'from' of > command > > @param is not found in the argument list of > > IMP::em::DensityMap::get_transformed_into(const DensityMap *source, const > > algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) > > build/include/IMP/em/DensityMap.h:582: warning: The following parameters > of > > IMP::em::DensityMap::get_transformed_into(const DensityMap *source, const > > algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) are > not > > documented: > > parameter 'source' > > build/include/IMP/em/EnvelopePenetrationRestraint.h:33: warning: The > > following parameters of > > > IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(Particles > > ps, DensityMap *em_map, Float threshold) are not documented: > > parameter 'threshold' > > build/include/IMP/em/FitRestraint.h:37: warning: The following > parameters of > > IMP::em::FitRestraint::FitRestraint(ParticlesTemp ps, DensityMap *em_map, > > FloatPair norm_factors=FloatPair(0., 0.), FloatKey > > weight_key=atom::Mass::get_mass_key(), float scale=1, bool > > use_rigid_bodies=true, KernelType kt=GAUSSIAN) are not documented: > > parameter 'kt' > > build/include/IMP/em/ImageHeader.h:60: warning: argument 'in' of command > > @param is not found in the argument list of > > IMP::em::ImageHeader::set_image_type(img_type im) > > build/include/IMP/em/ImageHeader.h:60: warning: The following parameters > of > > IMP::em::ImageHeader::set_image_type(img_type im) are not documented: > > parameter 'im' > > build/include/IMP/em/SampledDensityMap.h:74: warning: The following > > parameters of IMP::em::SampledDensityMap::project(const ParticlesTemp > &ps, > > int x_margin, int y_margin, int z_margin, algebra::Vector3D > > shift=algebra::Vector3D(0., 0., 0.), FloatKey > > mass_key=atom::Mass::get_mass_key()) are not documented: > > parameter 'ps' > > parameter 'mass_key' > > build/include/IMP/em/converters.h:73: warning: argument 'rad_key' of > command > > @param is not found in the argument list of > > IMP::em::SampledDensityMap::particles2binarized_density(const > ParticlesTemp > > &ps, Float resolution, Float apix, int sig_cutoff=3, const FloatKey > > &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/em/converters.h:54: warning: argument 'rad_key' of > command > > @param is not found in the argument list of > > IMP::em::SampledDensityMap::particles2density(const ParticlesTemp &ps, > Float > > resolution, Float apix, int sig_cutoff=3, const FloatKey > > &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/em/converters.h:101: warning: argument 'rad_key' of > > command @param is not found in the argument list of > > IMP::em::SampledDensityMap::particles2surface(const ParticlesTemp &ps, > Float > > apix, const FloatKey &weight_key=IMP::atom::Mass::get_mass_key()) > > build/include/IMP/isd/AmbiguousNOERestraint.h:25: warning: included file > > AmbiguousNOERestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/AmbiguousNOERestraint.h:26: warning: included file > > AmbiguousNOERestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/GaussianProcessInterpolation.h:41: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:43: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:45: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:46: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:49: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:50: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:51: warning: > expected > > whitespace after param command > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) > > build/include/IMP/isd/GaussianProcessInterpolation.h:40: warning: The > > following parameters of > > > IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(FloatsList > > x, Floats sample_mean, Floats sample_std, unsigned n_obs, > UnivariateFunction > > *mean_function, BivariateFunction *covariance_function, Particle *sigma, > > double sparse_cutoff=1e-7) are not documented: > > parameter 'x' > > parameter 'sample_mean' > > parameter 'sample_std' > > parameter 'n_obs' > > parameter 'mean_function' > > parameter 'covariance_function' > > parameter 'sigma' > > parameter 'sparse_cutoff' > > build/include/IMP/isd/GaussianRestraint.h:22: warning: included file > > GaussianRestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/GaussianRestraint.h:23: warning: included file > > GaussianRestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/ISDRestraint.h:28: warning: included file > > ISDRestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/LogicalORRestraint.h:24: warning: included file > > LogicalORRestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/LogicalORRestraint.h:25: warning: included file > > LogicalORRestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/LognormalRestraint.h:22: warning: included file > > LognormalRestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/LognormalRestraint.h:23: warning: included file > > LognormalRestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/MarginalHBondRestraint.h:31: warning: included file > > MarginalHBondRestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/MarginalHBondRestraint.h:32: warning: included file > > MarginalHBondRestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/MarginalNOERestraint.h:31: warning: included file > > MarginalNOERestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/MarginalNOERestraint.h:32: warning: included file > > MarginalNOERestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/MultivariateFNormalSufficient.h:52: warning: Found > > unknown command `\Sigma' > > build/include/IMP/isd/MultivariateFNormalSufficient.h:118: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:119: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:121: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:122: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:123: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:115: warning: The > > following parameters of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > MatrixXd &FX, double JF, const VectorXd &FM, const MatrixXd &Sigma, > double > > factor=1) are not documented: > > parameter 'FX' > > parameter 'JF' > > parameter 'FM' > > parameter 'Sigma' > > parameter 'factor' > > build/include/IMP/isd/MultivariateFNormalSufficient.h:129: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:130: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:132: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:133: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:134: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:135: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:136: warning: > expected > > whitespace after param command > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: > argument > > 'in' of command @param is not found in the argument list of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) > > build/include/IMP/isd/MultivariateFNormalSufficient.h:126: warning: The > > following parameters of > > > IMP::isd::MultivariateFNormalSufficient::MultivariateFNormalSufficient(const > > VectorXd &Fbar, double JF, const VectorXd &FM, int Nobs, const MatrixXd > &W, > > const MatrixXd &Sigma, double factor=1) are not documented: > > parameter 'Fbar' > > parameter 'JF' > > parameter 'FM' > > parameter 'Nobs' > > parameter 'W' > > parameter 'Sigma' > > parameter 'factor' > > build/include/IMP/isd/NOERestraint.h:27: warning: included file > > NOERestraint.h is not found. Check your EXAMPLE_PATH > > build/include/IMP/isd/NOERestraint.h:28: warning: included file > > NOERestraint.cpp is not found. Check your EXAMPLE_PATH > > build/include/IMP/multifit/coarse_molecule.h:50: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:50: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) > > build/include/IMP/multifit/coarse_molecule.h:51: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:50: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) > > build/include/IMP/multifit/coarse_molecule.h:53: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:50: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) > > build/include/IMP/multifit/coarse_molecule.h:54: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:50: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) > > build/include/IMP/multifit/coarse_molecule.h:55: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:50: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) > > build/include/IMP/multifit/coarse_molecule.h:50: warning: The following > > parameters of > > IMP::multifit::create_coarse_molecule_from_density(em::DensityMap *dmap, > > float dens_threshold, int num_beads, Model *mdl, float bead_radius) are > not > > documented: > > parameter 'dmap' > > parameter 'dens_threshold' > > parameter 'num_beads' > > parameter 'mdl' > > parameter 'bead_radius' > > build/include/IMP/multifit/coarse_molecule.h:16: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:16: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy > > &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:17: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:16: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy > > &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:18: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:16: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy > > &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:19: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:16: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy > > &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:20: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:16: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecule_from_molecule(const atom::Hierarchy > > &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:16: warning: The following > > parameters of IMP::multifit::create_coarse_molecule_from_molecule(const > > atom::Hierarchy &mh, int num_beads, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) are not documented: > > parameter 'mh' > > parameter 'num_beads' > > parameter 'mdl' > > parameter 'bead_radius' > > parameter 'add_conn_restraint' > > build/include/IMP/multifit/coarse_molecule.h:32: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:32: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:33: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:32: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:35: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:32: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:36: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:32: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:37: warning: expected > > whitespace after param command > > build/include/IMP/multifit/coarse_molecule.h:32: warning: argument > 'input' > > of command @param is not found in the argument list of > > IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) > > build/include/IMP/multifit/coarse_molecule.h:32: warning: The following > > parameters of IMP::multifit::create_coarse_molecules_from_molecules(const > > atom::Hierarchies &mhs, int frag_len, Model *mdl, float bead_radius, bool > > add_conn_restraint=false) are not documented: > > parameter 'mhs' > > parameter 'frag_len' > > parameter 'mdl' > > parameter 'bead_radius' > > parameter 'add_conn_restraint' > > build/include/IMP/multifit/fft_based_rigid_fitting.h:159: warning: > argument > > 'angle_sampling_interval' of command @param is not found in the argument > > list of IMP::multifit::fft_based_rigid_fitting(atom::Hierarchy mol2fit, > > em::DensityMap *dmap, double angle_sampling_interval_rad) > > build/include/IMP/multifit/fft_based_rigid_fitting.h:159: warning: The > > following parameters of > > IMP::multifit::fft_based_rigid_fitting(atom::Hierarchy mol2fit, > > em::DensityMap *dmap, double angle_sampling_interval_rad) are not > > documented: > > parameter 'angle_sampling_interval_rad' > > build/include/IMP/multifit/fitting_clustering.h:21: warning: argument > > 'pdb_filename' of command @param is not found in the argument list of > > IMP::multifit::fitting_clustering(const atom::Hierarchy &mh, const > > em::FittingSolutions &ts, float spacing, int top_sols, float rmsd) > > build/include/IMP/multifit/fitting_clustering.h:21: warning: The > following > > parameters of IMP::multifit::fitting_clustering(const atom::Hierarchy > &mh, > > const em::FittingSolutions &ts, float spacing, int top_sols, float rmsd) > are > > not documented: > > parameter 'mh' > > parameter 'top_sols' > > parameter 'rmsd' > > build/include/IMP/multifit/TransformationClustering.h:79: warning: > expected > > whitespace after param command > > build/include/IMP/multifit/TransformationClustering.h:75: warning: > argument > > 'in' of command @param is not found in the argument list of > > IMP::multifit::get_clustered(Particles ps, const > algebra::Transformation3Ds > > &trans, float max_rmsd, float max_angle_diff_in_rad, float max_displace, > int > > min_cluster_size) > > build/include/IMP/multifit/TransformationClustering.h:75: warning: The > > following parameters of IMP::multifit::get_clustered(Particles ps, const > > algebra::Transformation3Ds &trans, float max_rmsd, float > > max_angle_diff_in_rad, float max_displace, int min_cluster_size) are not > > documented: > > parameter 'trans' > > parameter 'max_displace' > > build/include/IMP/multifit/pca_based_rigid_fitting.h:28: warning: > argument > > 'rb_refine' of command @param is not found in the argument list of > > IMP::multifit::pca_based_rigid_fitting(core::RigidBody rb, Refiner > > *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey > > wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis > > dens_pca_input=algebra::PrincipalComponentAnalysis()) > > build/include/IMP/multifit/pca_based_rigid_fitting.h:28: warning: The > > following parameters of > > IMP::multifit::pca_based_rigid_fitting(core::RigidBody rb, Refiner > > *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey > > wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis > > dens_pca_input=algebra::PrincipalComponentAnalysis()) are not documented: > > parameter 'rb_refiner' > > build/include/IMP/multifit/RadiusOfGyrationRestraint.h:31: warning: > argument > > 'the' of command @param is not found in the argument list of > > > IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(Particles > > ps, int num_residues, Float scale=1.) > > build/include/IMP/multifit/RadiusOfGyrationRestraint.h:31: warning: The > > following parameters of > > > IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(Particles > > ps, int num_residues, Float scale=1.) are not documented: > > parameter 'num_residues' > > [generated]:0: warning: explicit link request to 'Object' could not be > > resolved > > build/include/IMP/saxs/RadiusOfGyrationRestraint.h:31: warning: The > > following parameters of > > IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(const > > Particles &particles, const Profile &exp_profile, const double end_q_rg= > > > > _______________________________________________ > > IMP-dev mailing list > > IMP-dev@salilab.org > > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >